Consortium Of Microbes Research Articles

Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds.

The capability of entomopathogenic fungi to live as plant endophytes is well established. However, their presence in undiscovered environmental niches represents the beginning of a new challenging research journey. Recently, Akanthomyces muscarius (Ascomycota, Cordycipitaceae) (Petch) Spatafora, Kepler & B. Shrestha was isolated from hazelnut buds infested by the big bud mite pest Phytoptus avellanae Nalepa, which makes the buds swollen, reddish, and unable to further develop. Gall formation is known to be regulated by a consortium of microbes and mites, and to better understand the possible role of A. muscarius within the infested gall, its whole genome sequence was obtained using a hybrid approach of Illumina and Nanopore reads. The functional and comparative genomics analysis provided within this study may help answer questions related to the ecology and the entomopathogenicity of this fungus.

Characterization of BrGH3A, a bovine rumen-derived glycoside hydrolase family 3 β-glucosidase with a permuted domain arrangement.

The bovine rumen contains a large consortium of residential microbes that release a variety of digestive enzymes for feed degradation. However, the utilization of these microbial enzymes is still limited because these rumen microorganisms are mostly anaerobes and are thus unculturable. Therefore, we applied a sequence-based metagenomic approach to identify a novel 2,445-bp glycoside hydrolase family 3 β-glucosidase gene known as BrGH3A from the metagenome of bovine ruminal fluid. BrGH3A β-glucosidase is a 92-kDa polypeptide composed of 814 amino acid residues. Unlike most glycoside hydrolases in the same family, BrGH3A exhibited a permuted domain arrangement consisting of an (α/β)6 sandwich domain, a fibronectin type III domain and a (β/α)8 barrel domain. BrGH3A exhibited greater catalytic efficiency toward laminaribiose than cellobiose. We proposed that BrGH3A is an exo-acting β-glucosidase from Spirochaetales bacteria that is possibly involved in the intracellular degradation of β-1,3-/1,4-mixed linkage glucans that are present in grass cell walls. BrGH3A exhibits rich diversity in rumen hydrolytic enzymes and may represent a member of a new clan with a permuted domain topology within the large family.

Pachyderm and petrichor: Searching for new ways to mitigate the human-elephant conflict

Geosmin, a taste and odor (T & O) compound that has been hypothesized to occur in higher magnitudes in water bodies due to climate change, is a water quality parameter for human consumption, but an olfactory cue for elephants to migrate towards water holes. It is proposed here to culture bacteria capable of geosmin biodegradation for the development of a unitary, or a consortium of microbes, to lower the geosmin content in human settlement-proximal water holes, to discourage the encroachment of elephants to villages.This novel idea aims to protect both, the elephant population and the human footprint in harm’s way, furnishing a program to conserve elephants while ensuring that human lives are protected. The environmental and social impacts of this proposed nature-based solution will be centered on 1. Elephant conservation 2. Reduction of incidences of the human-elephant conflict, which together provide a natural solution to a dilemma that so far has lacked tangible, sustainable, and long-term, bio-centric remedies.This editorial projects to protect both humans and elephants in a climate-change-impacted dry zone of Sri Lanka, where there are an estimated >5000-6000 elephants, which makes up 10% of the Asian elephant population in 2% of the range, the highest density of Asian elephants in any country. In an increasingly water-impoverished landscape, encroaching on human settlements for water and food flares up the human-elephant conflict that claims hundreds of lives across the human-animal divide, in any given year.There is a quote by arguably the greatest artist that walked on this earth, Pablo Picasso, who coined this wonderful line “God is really only another artist. He invented the giraffe, the elephant and the cat. He has no real style, He just goes on trying other things”. We scientists too need to be like artists – “try other things” to save the opulence of biodiversity – those giraffes, pachyderms and big cats, threatened by habitat expansion and human encroachment, of which the elephant holds the pinnacle rung. This editorial is simply a wake-up call for the scientific community to try other things.

Root powder extract, phytochemical studies & preparation of herbal formulation tinospora cordifolia asava

Asava, a traditional formulation in Ayurveda, is renowned for its superior preservation and enhanced therapeutic efficacy. This phenomenon is largely attributed to the intricate process of fermentation facilitated by a consortium of microbes. Microbial activity not only extends the shelf-life of Asava but also transforms its constituent ingredients into potent therapeutics through biotransformation. The alcohol-aqueous milieu generated during fermentation not only preserves the formulation but also facilitates improved drug delivery within the body. This milieu, predominantly produced by microbial action, acts as a medium for the potentization of drugs, enhancing their bioavailability and efficacy. Moreover, the biotransformation mediated by native microbes leads to the synthesis of novel compounds with enhanced therapeutic properties, thereby elevating the overall efficacy of Asava. The preservative properties inherent in these formulations, coupled with microbial-mediated potentization, underscore the significance of microbial fermentation in augmenting the therapeutic potential of Asava in Ayurveda.

BIODIVERSITY OF THE GUT MICROBIOTA OF Epilachna vigintioctopunctata USING ILLUMINA MiSEQ PLATFORM

The insect gut is a complex system colonized by a consortium of microbes whichshare a symbiotic relation with the host and also contribute to its growth, development, immunity and defense against its enemies, reproduction and speciation, thereby play a crucial role in its survival. Hence understanding the role of these bacteria is a crucial step for using them in microbial control of pests. In present study, a 16S microbiome profiling of gut of Epilachna vigintioctopunctata was carried out. The study revealed 553 operational taxonomic units (OTUs). The majority of bacterial OTUs belonged to the phylum Proteobacteria, followed by Bacteroidetes, Firmicutes and Actinobacteria. The majority of bacterial OTUs belonged to the family Halomonadaceae which was the most abundant taxa in larval gut. The study provides a baseline information on gut inhabiting microbes of E. vigintiocto punctata up to the genus level for most phyla.

Bile Salt Hydrolase Activity-Based Probes for Monitoring Gut Microbial Bile Acid Metabolism.

Bile acids are bioactive metabolites that are biotransformed into secondary bile acids by the gut microbiota, a vast consortium of microbes that inhabit the intestines. The first step in intestinal secondary bile acid metabolism is carried out by a critical enzyme, bile salt hydrolase (BSH), that catalyzes the gateway reaction that precedes all subsequent microbial metabolism of these important metabolites. As gut microbial metabolic activity is difficult to probe due to the complex nature of the gut microbiome, approaches are needed to profile gut microbiota-associated enzymes such as BSH. Here, we develop a panel of BSH activity-based probes (ABPs) to determine how changes in diurnal rhythmicity of gut microbiota-associated metabolism affects BSH activity and substrate preference. This panel of covalent probes enables determination of BSH activity and substrate specificity from multiple gut anerobic bacteria derived from the human and mouse gut microbiome. We found that both gut microbiota-associated BSH activity and substrate preference is rhythmic, likely due to feeding patterns of the mice. These results indicate that this ABP-based approach can be used to profile changes in BSH activity in physiological and disease states that are regulated by circadian rhythms.

Application of biofertilizer to realize sustainable agricultural program: a review

The agricultural sector is a force to encourages the rise in the economic level of an agricultural country, such as Indonesia. However, agricultural programs that are not followed carefully can undermine the order of an agrarian state. Therefore, the concept of sustainable agriculture was introduced and has become a commitment for many countries in the world. One application of sustainable agriculture is the use of effective and environmentally friendly fertilizers. Biofertilizer is considered an alternative to chemical fertilizers that have more advantages. Biofertilizers contain a consortium of microbes that are beneficial to plants. In addition, biofertilizers can improve soil fertility. Many studies prove the effectiveness of biofertilizers in increasing crop yields. Currently, biofertilizers have been widely used in Indonesia, but sometimes the potential of laboratory-tested biofertilizers cannot be found in the field. Another issue is shelf life. This review focused on the effectiveness and shelf life of the biofertilizer. In this review, we try to collect data from previous studies and compile it into a framework that can help overcome the constraints of biofertilizer applications. The analysis was carried out with the introduction of biofertilizers, constraints in the practice of their use, and strategies to overcome those obstacles. Obstacles to the use of biofertilizers can be overcome by selecting potential microbes in order to survive in the soil. The addition of organic matter can also be done to add nutrients to the soil. In addition, storage of the product under adjusted conditions can maintain its effectiveness.

Current insights into microbiome-based therapy. Review

Current insights into microbiome-based therapy. Review

Root microbiota of tea plants regulate nitrogen homeostasis and theanine synthesis to influence tea quality

The flavor profile of tea is influenced not only by different tea varieties but also by the surrounding soil environment. Recent studies have indicated the regulatory role of soil microbes residing in plant roots in nutrient uptake and metabolism. However, the impact of this regulatory mechanism on tea quality remains unclear. In this study, we showed that a consortium of microbes isolated from tea roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. Variations were observed in the composition of microbial populations colonizing tea roots and the rhizosphere across different seasons and tea varieties. By comparing the root microorganisms of the high-theanine tea variety Rougui with the low-theanine variety Maoxie, we identified a specific group of microbes that potentially modulate nitrogen metabolism, subsequently influencing the theanine levels in tea. Furthermore, we constructed a synthetic microbial community (SynCom) mirroring the microbe population composition found in Rougui roots. Remarkably, applying SynCom resulted in a significant increase in the theanine content of tea plants and imparted greater tolerance to nitrogen deficiency in Arabidopsis. Our study provides compelling evidence supporting the use of root microorganisms as functional microbial fertilizers to enhance tea quality.

EAAS AND WHEY PROTEIN MAY IMPROVE PHYSICAL FUNCTION OF OLDER ADULTS INDEPENDENTLY OF GUT MICROBIOME

Abstract Essential amino acids (EAAs) and dietary proteins are major nutritional supplements that support the growth and activity of gut microbes, contributing to the wellbeing of their host. We hypothesized that daily ingestion of EAAs or whey proteins for twelve weeks would improve the gut microbiome of older adults and thereby have a positive impact on their physical functioning. The stool samples were collected from the 40 subjects before and after consuming EAAs or whey proteins for twelve weeks and subjected to Illumina based 16S rRNA gene sequencing. In both groups, the most abundant families in order of relative abundance included: Bacteroidaceae, Ruminococcaceae, Lachnospiraceae, Rikenellaceae, and Prevotellaceae, which indicated that these subjects were able to maintain a dominant consortium of microbes in their guts that have been associated with healthy aging. Individual gut microbiome samples analysis with nonmetric multidimensional space (NMDS) showed that each individual was associated with its unique microbiome. The key finding of this study was a significant reduction of plasma Interleukin-18 binding protein (IL-18) in EAAs vs whey group (p < 0.003). It is plausible that the reduced level of inflammatory IL-18 contributed to improved intestinal immunity. Moreover, the reduced inflammation might have resulted in better muscle performance in the EAAs group vs whey as evidenced by six-minute walking distance (EAAs 92.55 ± 4.16 ft vs whey 47.46 ± 4.99 ft, p< 0.0001) at the completion of study. Future studies will need to explore the role of EAAs on gut microbiome mediated reduction of immune inflammation on physical function and aging.

Biological Ammonia Production via Anaerobic Fermentation of Soy Meal Protein.

Conventional ammonia production methods, notably the energy-intensive Haber-Bosch process, are costly and contribute substantially to about 2% of the world's CO2 emissions. This study focuses on the biological approach to convert protein to ammonia via hyper-ammonia-producing bacteria (HAB) fermentation. A consortium of ruminal microbes was employed in this work to ferment soybean meal protein under varying processing conditions. The parameters investigated included pH (7-11), inoculum concentrations (1-10%), substrate concentrations (5-20%), and fermentation time (0-168 h). Optimal conditions for microbial growth and biological ammonia production were observed at pH 7, fermentation duration of 72 h, inoculum concentration of 10%, and substrate concentration of 10%. ~8000 mg/L biological ammonia was produced following HAB fermentation. By leveraging the capabilities of rumen HAB, this study contributes to the ongoing efforts to develop environmentally friendly processes for ammonia production that will mitigate both economic and environmental concerns associated with traditional methods.

Converting waste to resource: Utilisation of elemental S and consortia of halo–alkaliphilic S–oxidisers for preparation of acidified compost from organic wastes

Utilising the acidulated manures is a reliable option for plant nutrition and managing alkalinity stress. This study characterizes the common wastes and their acidulation potential through consortia of microbes like Priestia aryabhattai, Stutzerimonas stutzeri and Pseudomonas chloritidismutans and elemental sulphur (S°). The poultry manure (PM) and pressmud (Pmud) were rich in N, P, and phenol with a narrow C/N ratio. The water–soluble total N (TNsol), dissolved organic N (DON), NO3−–N was greater in cattle manure. Acidulation of manure declined pH by 0.5–2.5 units and increased titratable acidity (TA) and equivalent alkalinity neutralisation potential (EANP) by 5034.8 and 2,805,732.3 me kg−1, respectively. The incubation for 28 days was optimum for acidulation. The water–soluble SO42−, Mg2+, and DOC were the key variables explaining variability in EANP. The rapid acidulation of manure using microbial consortia and S° could be a pragmatic approach for recycling and reusing the waste.

Probiotics Modulate Host Immune Response and Interact with the Gut Microbiota: Shaping Their Composition and Mediating Antibiotic Resistance.

The consortium of microbes inhabiting the human body, together with their encoded genes and secreted metabolites, is referred to as the "human microbiome." Several studies have established a link between the composition of the microbiome and its impact on human health. This impact spans local gastrointestinal inflammation to systemic autoimmune disorders and neurodegenerative diseases such as Alzheimer's and Autism. Some of these links have been validated by rigorous experiments that identify specific strains as mediators or drivers of a particular condition. Consequently, the development of probiotics to compensate for a missing beneficial microbe(s) has advanced and become popular, especially in the treatment of irritable bowel diseases and to restore disrupted gut flora after antibiotic administration. The widespread use of probiotics is often advocated as a natural ecological therapy. However, this perception is not always accurate, as there is a potential for unexpected interactions when administering live microbial cultures. Here, we designed this research to explore the intricate interactions among probiotics, the host, and microbes through a series of experiments. Our objectives included assessing their immunomodulatory effects, response to oral medications, impact on microbial population dynamics, and mediation of antibiotic resistance. To achieve these goals, we employed diverse experimental protocols, including cell-based enzyme -linked immunosorbent assay (ELISA), antibiotic susceptibility testing, antimicrobial activity assays, computational prediction of probiotic genes responsible for antibiotic resistance, polymerase chain reaction (PCR)-based validation of predicted genes, and survival assays of probiotics in the presence of selected oral medications. Our findings highlight that more than half of the tested probiotics trigger an inflammatory response in the Caco-2 cell line, are influenced by oral medications, exhibit antibacterial activity, and possess genes encoding antimicrobial resistance. These results underscore the necessity for a reevaluation of probiotic usage and emphasize the importance of establishing regulations to govern probiotic testing, approval, and administration.

Bacterial consortium development and optimization for crack controlling cement mortar

It is crucial to carry out repairs to protect concrete structures and prevent the ingress of pollutants through cracks and fractures. Recently, as a solution, biological additives have drawn more attention over the past ten years as admixtures to cement-based materials. Microbial calcite precipitation is a natural process that can fill cracks, reduce greenhouse gas emissions caused by human activities, and conserve natural resources. This study aimed to identify bacteria and create a consortium of microbes with the desired abilities for Microbiologically Induced Calcium Carbonate Precipitation (MICCP) from potential sources. The selection and screening of isolates for consortium preparation were conducted using a precipitation medium that contained calcium chloride, and the resulting precipitates were analyzed using SEM and XRD. The selected organisms for consortium preparation were identified using 16S r RNA sequencing as A2 - Brevibacillus reuszeri STV1702A2, A1 - Bacillus sp. STV1702A1, and C1 - Bacillus thuringiensis STV1702C1. Before adding the consortium to cement mortar, the bacterial ratio was optimized using the Mixture Design. The consortium was subsequently incorporated into the cement mortar, resulting in a 40–45% increase in mechanical properties compared to normal cement mortar mix and a 20–25% increase in properties compared to the positive control, Bacillus subtilis (MTCC441). The durability properties were also examined, concluding that bacterial consortium is a better option for offshore constructions, tunnels, and trenches.

The Use of Synthetic Microbial Communities to Improve Plant Health.

Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.

Taking the pulse: Bacterial responses to intermittent antibiotics

Bacterial species respond differently to consecutive antibiotic exposures with potential consequences on the host microbiome. In this issue of Cell Host & Microbe, Münch etal. investigate the effects of intermittent antibiotic treatments on specific bacteria using a consortium of microbes comprising a functional intestinal microbiota in germ-free mice.

Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses

Historically, Hawai‘i had few massive coral bleaching events, until two consecutive heatwaves in 2014–2015. Consequent mortality and thermal stress were observed in Kāne‘ohe Bay (O‘ahu). The two most dominant local species exhibited a phenotypic dichotomy of either bleaching resistance or susceptibility (Montipora capitata and Porites compressa), while the third predominant species (Pocillopora acuta) was broadly susceptible to bleaching. In order to survey shifts in coral microbiomes during bleaching and recovery, 50 colonies were tagged and periodically monitored. Metabarcoding of three genetic markers (16S rRNA gene ITS1 and ITS2) followed by compositional approaches for community structure analysis, differential abundance and correlations for longitudinal data were used to temporally compare Bacteria/Archaea, Fungi and Symbiodiniaceae dynamics. P. compressa corals recovered faster than P. acuta and Montipora capitata. Prokaryotic and algal communities were majorly shaped by host species, and had no apparent pattern of temporal acclimatization. Symbiodiniaceae signatures were identified at the colony scale, and were often related to bleaching susceptibility. Bacterial compositions were practically constant between bleaching phenotypes, and more diverse in P. acuta and M. capitata. P. compressa's prokaryotic community was dominated by a single bacterium. Compositional approaches (via microbial balances) allowed the identification of fine-scale differences in the abundance of a consortium of microbes, driving changes by bleaching susceptibility and time across all hosts. The three major coral reef founder-species in Kāne‘ohe Bay revealed different phenotypic and microbiome responses after 2014–2015 heatwaves. It is difficult to forecast, a more successful strategy towards future scenarios of global warming. Differentially abundant microbial taxa across time and/or bleaching susceptibility were broadly shared among all hosts, suggesting that locally, the same microbes may modulate stress responses in sympatric coral species. Our study highlights the potential of investigating microbial balances to identify fine-scale microbiome changes, serving as local diagnostic tools of coral reef fitness.

Thermodynamic sensitivity of ammonia oxidizers-driven N2O fluxes under oxic-suboxic realms

In terrestrial ecosystems, the nitrogen dynamics, including N2O production, are majorly regulated by a complex consortium of microbes favored by different substrates and environmental conditions. To better predict the daily, seasonal and annual variation in N2O fluxes, it is critical to estimate the temperature sensitivity of different microbial groups for N2O fluxes under oxic and suboxic conditions prevalent in soil and wetlands. Here, we studied the temperature sensitivity of two groups of ammonia oxidizers, archaea (AOA) and bacteria (AOB), in relation to N2O fluxes through both nitrification and nitrifier-denitrification pathways across a wide temperature gradient (10–55 °C). Using square root theory (SQRT) and macromolecular rate theory (MMRT) models, we estimated thermodynamic parameters and cardinal temperatures, including maximum temperature sensitivity (TSmax). The distinction between N2O pathways was facilitated by microbial-specific inhibitors (PTIO and C2H2) and controlled oxygen supply environments (oxic: ambient level; and suboxic: ∼4%). We found that nitrification supported by AOA (NtA) and AOB (NtB) dominated N2O production in an oxic climate, while only AOB-supported nitrifier-denitrification (NDB) majorly contributed (>90%) to suboxic N2O budget. The models predicted significantly higher optimum temperature (Topt) and TSmax for NtA and NDB compared to NtB. Intriguingly, both NtB and NDB exhibited significantly wider temperature ranges than NtA. Altogether, our results suggest that temperature and oxygen supply control the dominance of specific AOA- and AOB-supported N2O pathways in soil and sediments. This emergent understanding can potentially contribute toward novel targeted N2O inhibitors for GHG mitigation under global warming.

Biochar-Bacillus consortium for a sustainable agriculture: physicochemical and soil stability analyses

Biochar has various agricultural applications, including the promising use as a carrier for beneficial microorganisms. However, most recent research has demonstrated the possible attachment or immobilization of a single bacterial species onto biochar rather than a consortium of microbes for biotechnological applications. Thus, an assessment on the potential of oil palm kernel shell (OPKS) biochar as a biofilm-producing Bacillus consortium carrier through optimization study on the operating and environmental factors influencing the biofilm adhesion was conducted using response surface methodology (RSM) and the subsequent soil stability and storage potential of the formulation. The highest Bacillus population was observed at temperature 33 °C, agitation speed of 135 rpm, at a neutral pH of 7.5 with 10% (w/w) of sago starch as the co-carbon source. The adhesion of Bacillus on OPKS biochar following the optimized conditions fitted pseudo-second order (PSO) of kinetic modelling (R2 = 0.998). The optimized formulation was subjected to storage in different temperatures and in vitro soil incubation which revealed that the Bacillus biofilm-adhered OPKS biochar may be stored up to 4 months with minimum range of live Bacillus viability reaching 107 CFU g-1 of biochar which is within the minimum range of acceptable biofertilizer viability (106 CFU mL-1). Formulation that is viable in room storage can be easily incorporated into current agricultural distribution networks that do not have refrigeration. This work highlighted the physicochemical and soil stability qualities of optimized Bacillus consortium adhesion on biochar for agricultural usage.Article HighlightsIntegration of biochar with Bacillus consortium biofilms served as novel organic fertilizer in agriculture.The biochar-integrated Bacillus biofilms persisted in challenging temperature and environment.Biochar-integrated Bacillus biofilm fertilizer fostered the attainment of the Sustainable Development GoalsGraphical

Development of Bacterial consortia from traditional lime mortar for the preparation of sustainable and strength-enhanced concrete: A solution for heavy metal toxic concrete

<p>The microbial consortia incorporated in bio concrete should have traits such as high alkali resistance and the ability to form endospores to overcome the mechanical and chemical stresses produced during concrete preparation. The primary intent of our work is to segregate and identify the calcium carbonate precipitating microorganisms with a strong urease activity, compare their potential for the preparation of bio concrete, and evaluate its performance, durability, and effects on heavy metal toxicity. Bacteria, algae, protozoans, yeasts, and fungi are predominantly reported in the consortia of microbes in a construction sample, making it an excellent source of wild microbial species and strains which have adapted to the environment of the construction place which consists of a consortium of limestone, fine sand, and curing water. Consortia of organisms were isolated from fermented lime mortar and curing construction water, which was recognized using the 16S rRNA gene sequencing technique. Atomic Absorption Spectrometry[AAS] and Inductively Coupled Plasma Mass Spectrometry[ICP-MS] were carried out to analyze the deduction of heavy metal toxicity present in the produced bio concrete. The results of strength and toxicity tests were compared with bio-concrete produced from standard cultures of Bacillus megaterium (NDRI-067) and Bacillus licheniformis(NDRI-598) obtained from the National Dairy Research Institute. (NDRI), and also compared with conventional concrete.</p>